1.0.0

API changes

Modules

• Renamed:
  • compute.big_phi to compute.network
  • compute.concept to compute.subsystem
  • models.big_phi to models.subsystem
  • models.concept to models.mechanism

Functions

• Renamed:
  • compute.main_complex() to compute.major_complex()
  • compute.big_mip() to compute.sia()
  • compute.big_phi() to compute.phi()
  • compute.constellation() to compute.ces()
  • compute.conceptual_information() to compute.conceptual_info()
  • subsystem.core_cause() to subsystem.mic()
  • subsystem.core_effect() to subsystem.mie()
  • subsystem.mip_past() to subsystem.cause_mip()
  • subsystem.phi_mip_past() to subsystem.phi_cause_mip()
  • subsystem.phi_mip_future() to subsystem.phi_effect_mip()
  • distance.small_phi_measure() to distance.repertoire_distance()
  • distance.big_phi_measure() to distance.system_repertoire_distance()
  • For all functions in convert:
    • loli to le (little-endian)
    • holi to be (big-endian)
• Removed compute.concept(); use Subsystem.concept() instead.

Arguments

• Renamed connectivity_matrix keyword argument of Network() to cm

Objects

• Renamed BigMip to SystemIrreducibilityAnalysis

  • Renamed the unpartitioned_constellation attribute to ces
  • sia is used throughout for attributes, variables, and function names
    instead of big_mip

• Renamed Mip to RepertoireIrreducibilityAnalysis

  • Renamed the unpartitioned_repertoire attribute to repertoire
  • ria is used throughout for attributes, variables, and function names
    instead of mip

• Renamed Constellation to CauseEffectStructure

  • ces is used throughout for attributes, variables, and function names
    instead of constellation

• Renamed Mice to MaximallyIrreducibleCauseOrEffect

  • mic or mie are used throughout for attributes, variables, and function
    names instead of mip

• Similar changes were made to the actual and models.actual_causation
  modules.

Configuration settings

• Changed configuration settings as necessary to use the new object names.

Constants

• Renamed Direction.PAST to Direction.CAUSE
• Renamed Direction.CAUSE to Direction.EFFECT

API additions

Configuration settings

• Added CACHE_REPERTOIRES to control whether cause/effect repertoires are
  cached. Single-node cause/effect repertoires are always cached.
• Added CLEAR_SUBSYSTEM_CACHES_AFTER_COMPUTING_SIA to control whether
  subsystem caches are cleared after calling compute.sia().

Objects

• Added two new objects, MaximallyIrreducibleCause and
  MaximallyIrreducibleEffect, that are subclasses of
  MaximallyIrreducibleCauseOrEffect with a fixed direction.

Refactor

• Moved network-level functions in compute.big_phi to
  pyphi.compute.network
• Moved subsystem-level functions in compute.big_phi and compute.concept to
  compute.subsystem

Documentation

• Added a description of TPM representations.
• Improved the explanation of conditional independence and updated the example
  to reflect that PyPhi now raises an error if a conditionally-dependent TPM is
  provided.
• Added detailed installation instructions.
• Little-endian and big-endian replace LOLI and HOLI terminology
• Added documentation for the following modules:
  • distribution
  • cache
  • compute.parallel
  • compute top-level module
  • module top-level module